Table 3.

Characterization of modules and network when estimating networks by GL and by using density, centralization and heterogeneity (edges’ stability has been used as weight) in plant data

Module	Density	Centralization	Heterogeneity	Nr nodes	Color coded
${\mathcal{N}}_O$ a
Module 1b	0.51	0.33	0.37	7	Brown
Module 2c	0.39	0.25	0.40	6	Yellow
Module 3d	0.23	0.19	0.48	10	Blue
Module 4e	0.22	0.19	0.46	10	Turquoise
Complete	0.05	0.07	0.71	54
${\mathcal{N}}_G$ f
Module 5g	0.49	0.33	0.41	7	Yellow
Module 6h	0.37	0.23	0.31	9	Turquoise
Module 7i	0.29	0.33	0.48	8	Brown
Module 8j	0.25	0.21	0.44	9	Blue
Complete	0.05	0.07	0.77	48

^aNetwork using the original metabolite values

^bModule 1: glutamine, isoleucine, lysine, pyroglutamic acid, threonine, tyrosine, valine

^cModule 2: allantoine, galactinol, glycine, leucine, raffinose , succinic acid

^dModule 3: 2-aminoadipic acid, alanine, aspartate, beta-alanine, citrate, methionine, phenylalanine, proline, perine, tryptophan

^eModule 4: 5-aminocarboxy-4,6-dihydroxypyrimidine, ascorbic acid, fructose, fructose-6-phospate, glucose-6-phosphate, glyceric acid, glycerol, monomethylphosphate, pentonic acid, phosphoric acid, sucrose, threonate, urea

^fNetwork using genotypic-related information

^gModule 5: glutamine, glyceric acid, isoleucine, leucine, monomethylphosphate, valine, xylose

^hModule 6: ascorbic-acid, aspartate, glycine, phenylalanine, proline, pyroglutamic acid, raffinose, serine, succinic acid

ⁱModule 7: alanine, fructose-6-phospate, fumarate, glucose-6-phosphate, lysine, threonate, threonine, tyrosine

^jModule 8: allantoine, asparagine, galactinol, glycerol, pentonic acid, phosphoric acid, suberyl-glycine, sucrose, urea